MineGraph facilitates plastid and mitochondrial graph pangenome analysis in plants

The rapid growth of genomic sequencing is driving the implementation of graph pangenomes in evolutionary studies, yet the computational costs and complex interpretations at higher taxonomic levels hinder their broad use. Here, we present an evolutionary graph pangenome (evograph) pipeline to streamline diversity analyses across species and families. Applying this framework to 709 Poales chloroplast genomes indicates that genomic diversity is driven primarily by species-specific variation. We resolve a 77.7 Kbp consensus genome and apply graph theory metrics to highlight distinct genus-level evolutionary signatures. Evographs provide a powerful, nuanced framework for resolving evolutionary complexity across high taxonomic levels.